chr20-25215277-T-C

Variant names:

• chr20-25215277-T-C
• rs2073077
• NM_001247.5:c.673+335T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001247.5(ENTPD6):​c.673+335T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,106 control chromosomes in the GnomAD database, including 5,440 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (5440 hom., cov: 33)
• Consequence: ENTPD6 NM_001247.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 7 publications found

Genes affected

ENTPD6 (HGNC:3368): (ectonucleoside triphosphate diphosphohydrolase 6) ENTPD6 is similar to E-type nucleotidases (NTPases). NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD6 contains 4 apyrase-conserved regions which are characteristic of NTPases. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001247.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD6	NM_001247.5	MANE Select	c.673+335T>C		intron	N/A	NP_001238.3
	ENTPD6	NM_001322378.2		c.673+335T>C		intron	N/A	NP_001309307.2
	ENTPD6	NM_001317941.3		c.670+335T>C		intron	N/A	NP_001304870.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD6	ENST00000376652.9	TSL:1 MANE Select	c.673+335T>C		intron	N/A	ENSP00000365840.4
	ENTPD6	ENST00000360031.6	TSL:1	c.670+335T>C		intron	N/A	ENSP00000353131.2
	ENTPD6	ENST00000354989.10	TSL:1	c.589+335T>C		intron	N/A	ENSP00000347084.6

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36053 AN: 151988 Hom.: 5425 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.237 AC: 36101 AN: 152106 Hom.: 5440 Cov.: 33 AF XY: 0.235 AC XY: 17495 AN XY: 74368

African (AFR) AF: 0.411 AC: 17027 AN: 41458

American (AMR) AF: 0.168 AC: 2568 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2278 AN: 5176

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10473 AN: 67974

Other (OTH) AF: 0.201 AC: 426 AN: 2116

Alfa AF: 0.214 Hom.: 1952

Bravo AF: 0.245

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2073077; hg19: chr20-25195913;